Penn State researchers in the Center for Quantitative Imaging (CQI) used advanced image processing to create high-resolution computer-generated 3D models, called meshes, and visualizations of polychaete worms for the Smithsonian Institution. The digital models of these aquatic segmented worms preserve the biological specimens in detail and allow researchers worldwide to examine key anatomical features without handling the original material.
Odette Mina, director of the Institute of Energy and the Environment's laboratories, and Michelle Quigley, assistant research professor and lead researcher at CQI, spoke about how the imaging and digital reconstruction process works and why non-destructive, high-resolution X-ray computed tomography (CT) is changing how scientists study, preserve and access complex specimens.
Q: For those unfamiliar with the Center for Quantitative Imaging, what does this lab make possible and why does it matter?
Mina: CQI is a specialized facility that uses advanced X-ray computed tomography to create high-resolution, three-dimensional images of objects, from tiny biological specimens to large geological ones, and synthetic samples, without destroying them. This allows researchers to visualize complex systems in 3D and quantify detailed internal structures, like porosity. In short, CQI turns what's invisible into something measurable and visually compelling, enabling discoveries across biology, geology, engineering and cultural heritage.
Q: What was the goal of creating these scans and digital models?
Quigley: For a new species to be identified, researchers need to compare new specimens to a type specimen, which is the original reference specimen, the standard scientists use to decide whether something is truly new or already known. This traditionally requires travel to the Smithsonian or shipping the type specimen to the researcher. Many scientists who study polychaete worms are located outside the U.S., where travel or shipping can be difficult or impossible. These scans, meshes and videos allow researchers anywhere in the world to access the type specimens without those barriers, improving access and encouraging taxonomic work globally.
Q: How did the collaboration between Penn State and the Smithsonian come about?
Mina: The collaboration began in 2022 when Smithsonian researchers identified CQI as an ideal partner to digitally preserve specimens from the National Museum of Natural History. The Smithsonian trusts Penn State with its specimens and its data. That level of trust signals confidence in CQI's ability to deliver world-class imaging with precision, care and scientific rigor. It shows that the lab is equipped not only with cutting-edge technology but also with the expertise needed to handle irreplaceable and scientifically significant materials. This collaboration underscores CQI's role as a leader in non-destructive imaging and quantitative analysis that meets the highest standards for research, preservation and public engagement.
Q: Turning raw CT scans into usable 3D meshes and videos sounds complex. What does that process involve?
Quigley: It takes extensive image processing. First, the specimen must be separated from the rest of the scan, which can be challenging depending on the specimen's condition and scan quality. Gaps may need to be closed if parts were removed or degraded, and features like scales can be difficult to isolate. Once separated, the specimen is turned into a mesh, a detailed polygon-based digital model that represents the geometry of an object. For visualizations, the specimen is then manipulated in 3D - rotated, sliced or moved - to highlight the features most important for identification and taxonomy.
Q: While this project focused on simple organisms, how do these same imaging and reconstruction techniques apply to other research areas?
Mina: The same capabilities are incredibly versatile. In geosciences, they can reveal pore networks in rocks or soils to study fluid flow or carbon storage. In engineering and materials science, they can identify defects or internal architecture in composites or metals. In biology and medicine, they allow detailed study of plant roots, insects or small vertebrates. Lastly, in cultural heritage, they support digital preservation of fossils and artifacts. CQI's technology makes it possible to see inside virtually any object, non-destructively, and create precise, quantitative 3D models.
Q: Why is the ability to digitally "move through" a specimen so powerful compared to traditional images?
Quigley: Static images restrict you to specific views, which can cause important context to be lost. By moving through an organism, you can observe transitions - such as how different anatomical structures change along the body - or examine how features attach from multiple angles. CT imaging also reveals interior structures that photographs or drawings don't capture at all. Being able to explore a specimen in 3D provides a more complete understanding of a specimen's anatomy and taxonomic variation.
